Contacts of the helix formed by residues 499 - 513 (chain A) in PDB entry 5ID6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 499 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A GLU* 3.4 22.3 + - - +
314A ILE* 4.0 13.5 - - + -
495A ASP 4.3 7.0 + - - +
496A ILE* 2.7 47.5 + - - +
498A LEU* 1.3 84.4 - - + +
500A VAL* 1.3 60.7 + - - +
501A ASP 3.1 1.6 + - - -
502A HIS* 3.5 9.4 + - - +
503A ILE* 3.5 23.5 + - + +
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Residues in contact with VAL 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU* 4.7 6.1 - - + -
314A ILE* 3.4 34.8 - - + -
460A LEU* 5.1 8.1 - - + +
463A VAL* 3.8 15.3 - - + -
464A LYS* 4.3 29.2 - - + +
467A GLU* 4.4 14.4 - - + +
497A LEU* 3.1 18.6 - - + +
498A LEU 3.0 1.2 - - - -
499A LYS* 1.3 77.1 - - - +
501A ASP* 1.3 61.0 - - - +
502A HIS 3.5 0.2 - - - -
503A ILE* 3.8 9.5 - - + +
504A TYR* 2.9 31.4 + - + +
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Residues in contact with ASP 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS* 3.0 37.3 + - - +
467A GLU* 5.2 1.8 - - - +
498A LEU* 3.0 17.3 + - + +
500A VAL* 1.3 83.0 - - + +
502A HIS* 1.3 65.7 + - - +
504A TYR* 3.2 2.5 + - - +
505A ASP* 3.1 40.5 + - - +
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Residues in contact with HIS 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU* 3.2 50.0 + - + +
498A LEU 4.5 0.2 + - - -
499A LYS* 3.5 9.7 + - - +
501A ASP* 1.3 80.9 + - - +
503A ILE* 1.3 66.8 + - + +
505A ASP* 3.2 7.5 + - - +
506A ALA* 3.0 24.2 + - + +
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Residues in contact with ILE 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU 4.1 17.0 - - - +
303A VAL* 3.6 26.7 - - + -
304A PHE* 5.6 0.4 - - - -
307A THR* 3.9 29.8 - - + +
308A LEU* 4.7 4.5 - - + -
314A ILE* 5.3 3.4 - - + -
460A LEU* 4.3 11.4 - - + -
499A LYS* 3.5 16.8 - - + +
500A VAL* 3.5 10.7 + - - +
501A ASP 3.3 0.8 - - - -
502A HIS* 1.3 81.4 - - + +
504A TYR* 1.3 65.9 + - - +
506A ALA* 3.2 0.9 + - - +
507A ILE* 3.0 46.1 + - + +
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Residues in contact with TYR 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LYS* 4.8 0.9 + - - -
460A LEU* 3.7 38.8 - - + +
461A ASP* 2.6 33.7 + - - -
464A LYS* 3.8 28.7 - - + -
500A VAL 2.9 18.8 + - - +
501A ASP* 3.4 5.2 - - - +
503A ILE* 1.3 77.9 - - - +
505A ASP* 1.3 74.7 + - - +
507A ILE* 3.4 1.9 + - - +
508A ARG* 3.0 41.4 + - + +
890A TRP* 3.0 34.7 + + - -
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Residues in contact with ASP 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LYS* 6.1 0.5 - - - -
501A ASP* 3.1 30.9 + - - +
502A HIS* 3.2 9.3 + - - +
504A TYR* 1.3 85.8 - - - +
506A ALA* 1.3 57.3 + - - +
508A ARG* 3.3 33.5 + - - +
509A ASN* 2.9 40.8 + - - +
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Residues in contact with ALA 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A GLU* 3.5 40.6 - - + +
293A GLY* 4.1 2.9 - - - +
294A TYR* 4.4 15.0 + - + +
502A HIS* 3.0 20.6 + - + +
503A ILE 3.8 0.7 - - - +
505A ASP* 1.3 74.1 - - - +
507A ILE* 1.3 66.4 + - - +
509A ASN* 3.4 8.8 + - - +
510A TYR* 3.2 23.2 + - - +
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Residues in contact with ILE 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A GLU 4.0 13.2 - - - +
293A GLY* 5.5 0.9 - - - -
300A VAL* 4.3 30.3 - - + +
303A VAL* 5.3 0.7 - - + -
304A PHE* 4.3 27.4 - - + +
456A MSE 4.7 11.0 - - + -
460A LEU* 4.1 16.2 - - + -
503A ILE* 3.0 34.7 + - + +
504A TYR 4.0 2.2 - - - +
506A ALA* 1.3 75.7 - - - +
508A ARG* 1.3 62.6 + - - +
510A TYR* 3.3 7.5 + - - +
511A VAL* 3.1 26.7 + - + +
890A TRP* 4.1 19.7 - - + -
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Residues in contact with ARG 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A TYR* 3.0 32.8 + - + +
505A ASP* 3.3 36.2 + - - +
507A ILE* 1.3 76.1 - - - +
509A ASN* 1.3 81.3 + - - +
511A VAL* 3.9 0.9 - - - +
512A THR* 2.9 38.8 + - - +
890A TRP* 3.5 55.3 - - + +
894A GLU* 6.6 0.2 - - - -
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Residues in contact with ASN 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 6.2 3.1 - - + -
505A ASP* 2.9 31.7 + - - +
506A ALA* 3.8 7.8 - - - +
507A ILE 3.4 0.2 - - - -
508A ARG* 1.3 94.5 + - - +
510A TYR* 1.3 61.8 + - - +
512A THR* 3.9 10.6 - - - +
513A GLN* 3.2 24.8 + - - +
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Residues in contact with TYR 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A TYR* 3.3 44.6 - - - +
295A THR 3.9 4.0 + - - -
296A SER* 3.3 15.7 - - - -
297A ASP* 2.8 38.4 + - - -
300A VAL* 3.6 24.5 - - + -
446A LEU* 4.1 16.4 - - + -
447A LYS* 4.3 10.2 - - + +
506A ALA 3.2 12.6 + - - +
507A ILE 3.5 8.5 - - - +
508A ARG 3.2 0.4 - - - -
509A ASN* 1.3 75.8 - - - +
511A VAL* 1.3 72.1 + - + +
513A GLN* 3.3 34.0 - - - +
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A VAL* 6.1 0.2 - - + -
446A LEU* 5.4 7.2 - - + -
447A LYS* 2.8 46.4 + - + +
453A VAL* 4.0 35.9 - - + -
456A MSE 6.3 1.8 - - - -
507A ILE* 3.1 20.0 + - + +
510A TYR* 1.3 84.3 - - + +
512A THR* 1.3 58.5 + - - +
890A TRP* 4.0 29.2 - - + -
891A THR* 3.9 19.4 - - + +
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Residues in contact with THR 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LYS* 4.5 2.1 + - - -
508A ARG* 2.9 25.6 + - + +
509A ASN* 4.1 12.6 - - - +
510A TYR 3.2 0.2 - - - -
511A VAL* 1.3 76.4 - - - +
513A GLN* 1.3 65.1 + - - +
514A LYS* 3.7 1.7 + - - +
890A TRP* 3.9 22.5 + - - +
891A THR* 4.4 6.8 - - - +
894A GLU* 3.4 42.0 - - + +
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Residues in contact with GLN 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A TYR 5.2 2.3 - - - +
447A LYS* 3.3 23.6 + - + +
509A ASN 3.2 13.2 + - - +
510A TYR* 3.3 35.8 - - - +
511A VAL 3.3 0.2 - - - -
512A THR* 1.3 80.4 - - - +
514A LYS* 1.3 76.9 + - - +
515A PRO* 3.7 0.5 - - - +
516A TYR 4.3 9.0 + - - +
517A SER* 5.1 8.7 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il